GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Herbaspirillum seropedicae SmR1

Align Succinylornithine transaminase; SOAT; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase

Query= curated2:Q3Z295
         (406 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05420 HSERO_RS05420
           4-aminobutyrate aminotransferase
          Length = 426

 Score =  225 bits (573), Expect = 2e-63
 Identities = 148/403 (36%), Positives = 209/403 (51%), Gaps = 37/403 (9%)

Query: 23  FIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEP 82
           F   R   + LWD +G+ +IDFA GIAV   GH HP+L +A+  Q  KF HT   Y   P
Sbjct: 28  FYAERAANAELWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFTHTA--YQIVP 85

Query: 83  V---LRLAKK---LIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKN 136
               + LA++   L    +  +  F ++GAEA E A+K+AR  AH    + + G++AF  
Sbjct: 86  YASYVELAERINRLTPGNYPKKTAFFSTGAEAVENAIKIAR--AH----TGRPGVIAFAG 139

Query: 137 AFHGRTLFTVSAGGQPA-YSQDFAPLPPDIRHAAY----NDINSASALID---------- 181
            FHGRT+  ++  G+ A Y   F P P D+ HA Y    + I S  AL            
Sbjct: 140 GFHGRTMMGMALTGKVAPYKLGFGPFPGDVFHAPYPSALHGITSEDALEAVKGLFKSDIE 199

Query: 182 -DATCAVIVEPIQGEGGVVPASNAFLQGLRELCDRHNALLIFDEVQTGVGRTGELYAYMH 240
                A+I+EP+QGEGG   A   F++GLR LCD H  LLI DEVQ+G GRTG+L+A  H
Sbjct: 200 AKRVAAIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEH 259

Query: 241 YGVTPDLLTTAKALGGGFPVGALLTTEECASVMTVGTHGTTYGGNPLASAVAGKVLELIN 300
           Y V PDL+T AK+L GG P+ A+    E       G  G TY GNPLA A A  VL+++ 
Sbjct: 260 YDVLPDLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLGGTYAGNPLAIASALAVLDVME 319

Query: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQ-----AKQIS 355
             +++   ++  D   E L  +       +EVRG+G ++         G+      K++ 
Sbjct: 320 EEQLVTRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAVEFADPATGKPDAEYTKKVQ 379

Query: 356 QEAAKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFAAA 396
           Q A   G+++L  G  GNV+RF   L + +  +   L   A A
Sbjct: 380 QHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMDEALGILAKA 422


Lambda     K      H
   0.319    0.136    0.408 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 497
Number of extensions: 27
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 406
Length of database: 426
Length adjustment: 31
Effective length of query: 375
Effective length of database: 395
Effective search space:   148125
Effective search space used:   148125
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory